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Verkko v2.3
These are release notes for Verkko version 2.3, which was released on December 5th, 2025. Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO or hifiasm corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.
The source code distribution contains everything you need to create a binary distribution for your own specific OS. Please report any issues you encounter.
Citation
- Rautiainen M, Nurk S, Walenz BP, Logsdon GA, Porubsky D, Rhie A, Eichler EE, Phillippy AM, Koren S. Telomere-to-telomere assembly of diploid chromosomes with Verkko. Nat Biotech. (2023). doi:10.1038/s41587-023-01662-6
- Antipov D, Rautiainen M, Nurk S, Walenz BP, Solar SJ, Phillippy AM, Koren S. Verkko2 integrates proximity ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding. Genome Research (2025). doi:10.1101/gr.280383.124
Minimum Requirements
- 8GB minimum memory; 16GB strongly suggested
- GCC 9 or newer (for compilation only)
- Rust (v1.74+) (for compilation only)
- Python (v3.10+), with biopython, parasail, and networkx modules
- Snakemake >=7.0, <8.0
- bamtools >=2.5.2
- MashMap 2.0 or newer (for filtering known sequences and Hi-C)
- GraphAligner v1.0.19 or newer
- Winnowmap
- For Hi-C/PoreC phasing:
Installation
Users can download Verkko as source code or installed through a package manager like conda. The source code package needs to be compiled and installed before it can be used. Do NOT download the .zip source code. It is missing files and will not compile. This is a known flaw with git itself.
Run either:
install from conda
conda install -c conda-forge -c bioconda -c defaults verkko
or build from source
curl -L https://github.com/marbl/verkko/releases/download/v2.3/verkko-v2.3.tar.gz --output verkko-v2.3.tar.gz
md5sum verkko-v2.3tar.gz
Confirm the MD5 for the tar.gz matches expected: 9c94f1a60b500907724cdc70fd7d9bf2 verkko-v2.3.tar.gz and compile:
tar -xzf verkko-v2.3.tar.gz
cd verkko-v2.3/src
make -j 8
cd ..
Verkko will be installed in verkko-v2.3/bin. You can move the contents to verkko-v2.3/bin/* and verko-v2.3/lib/* to a central location if you would like. If GraphAligner, Winnowmap, MashMap, bwa, or samtools are not available in your path, you may also symlink them under verkko-v2.3/lib/verkko/bin/
See the README for more details.
Updates
Verkko v2.3 IS NOT (expected to be) compatible with assemblies started with Verkko v2.2.1 nor any earlier version. We DO NOT recommend mixing versions.
- Update consensus algorithm to improve final assembly QV.
- Fix lost heterozygosity in simple-sequence repeats. When both ONT and HiFi are available but HiFi cannot be assigned to a haplotype, rely on longer ONT reads to generate consensus.
- Handle mixed HiFi and correct ONT datasets better, prioritizing HiFi data during consensus.
- Refactor and clean-up Hi-C phasing and improve phasing of non-diploid components (e.g. X and Y chromosomes)
- Output BAM files report MAPQ to indicate which reads had multiple placements in the assembly to distinguish homozygous or assignable reads.
- Simplify --paths usage to auto-inherit read paths from the previous assembly rather than specifying them again.
Bug Fixes
Known Issues
See the issues page for up-to date open issues, or to report a problem.
- Long runtime of MBG and high disk usage in overlapping with very high HiFi coverage (>200x). We recommend downsampling to 100x.
- Slow consensus package build on HiFi-only or very fragmented assemblies due to being I/O bound, will be addressed in a future release.
- Prioritization of HiFi data over corrected ONT data for consensus is currently based on read name, assuming HiFi data starts with an 'm' and number indicating the instrument ID.
Legal
See the README.licenses file and individual source code files for details.